Re: [ccp4bb] tNCS: indexing and EP problems
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Nicolas, you need to make sure the SPACE_GROUP_NUMBER is set (not commented out) and different from 0 in order for UNIT_CELL_PARAMETERS to be taken into account. Additionally you can unset the refinement of the CELL in the respective REFINE(IDXREF) instruction. Regards, Tim On 09/23/2013 05:51 PM, Nicolas Soler wrote: Thanks for your answers, I realized too late that my question number 2 was misleading. I wondered in fact whether shelxd or another program could handle tNCS fine. Otherwise for my indexing concerns, I have been trying to feed xds with the unit cell parameters found by mosflm via the UNIT_CELL_CONSTANTS keyword in XDS.INP but I didn't find them back in the solution list proposed by IDXREF.LP. Has anybody had similar issues? Cheers, Nicolas On 23/09/2013 15:22, Tim Gruene wrote: Dear Nicolas, shelxd is one answer to question 2 (http://shelx.uni-ac.gwdg.de/SHELX/shelxd_mm_keywords.php: PATS). I am sure there are others. You can provide the cell from mosflm to XDS. If you want XDS to find the cell without this information, there are plenty of keywords to tweak, although in my experience it is often sufficient to find a decent set of images to collect spots from, play with the things you let XDS refine (REFINE(...)) and finding the correct ORGX and ORGY. In difficult cases I use adxv to get an estimate for the cell dimensions to judge whether or not XDS found the correct one. Best, Tim On 09/23/2013 04:04 PM, Nicolas Soler wrote: Dear experts, I am dealing at the moment with a case involving translated NCS copies of my asymmetric unit along one axis of the unit cell (3 clear non-origin peaks in the native Patterson). I could get Mosflm to find the corresponding big unit cell only after restricting the max deviation from integral hkl parameter to 0.1 and thus get the majority of the spots under prediction boxes (although the cell parameters don't look very accurate sometimes). I have 2 questions about it : 1) Do you know whether it would be possible to configure XDS the same way, to make it find this enlarged unit cell ? (no success so far...) 2) Are you aware of any experimental phasing program making use of the information provided by the Patterson for finding the substructure? Many thanks in advance, Nicolas -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSQTmOUxlJ7aRr7hoRAmcZAKDR7j+rt/z408FXlN92EW64fjhRNgCfTo0v UYe3fqRklf6llglhUJbumgA= =q1BH -END PGP SIGNATURE-
[ccp4bb] Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology (October 22, 2013) and PSI Workshop on Theoretical Model Archiving and Validation (October 21, 2013)
*Workshop on the PDBx/mmCIF Data Exchange Format For Structural Biology* Center For Integrative Proteomics Research Rutgers, The State University of New Jersey Tuesday October 22, 2013 http://www.proteinmodelportal.org/workshop-2013/ The wwPDB has established PDBx/mmCIF as the new standard format for data exchange and archiving in structural biology (http://www.wwpdb.org/news/news_2013.html#22-May-2013). To help facilitate the transition from PDB to PDBx/mmCIF format the wwPDB is organizing a programmer's workshop describing the content and organization of PDBx/mmCIF data, and the available software tools and libraries supporting PDBx/mmCIF (C/C++, Java, and Python). The workshop will be held on Tuesday, October 22, 2013 at Rutgers, The State University of New Jersey (in conjunction with a PSI Workshop on Theoretical Model Archiving and Validation to be held Monday, October 21, 2013): Starting at 9am, the morning session will include presentations from: Paul Adams (Phenix), David Case (AMBER), Tom Goddard (UCSF Chimera), Robert Hanson (JMol), Eugene Krissinel (CCP4/mmdb), Andreas Prilic (BioJava), John Westbrook (RCSB PDB). The afternoon session will offer an opportunity to work hands-on with the presenters and developers in the areas of structural biology and molecular modeling to learn application details and to discuss successful approaches and experiences in adapting software to support PDBx/mmCIF. In addition, the workshop will include a discussion of PDBx/mmCIF extensions required to represent molecular modeling specific information. There is no registration fee, but online registration is required (registration Deadline is October 4). For detailed agenda and online registration: http://www.proteinmodelportal.org/workshop-2013/ Looking forward to welcoming you at the workshop, Andrej Sali, John Westbrook, and Torsten Schwede Prof. Dr. Torsten Schwede Biozentrum Universität Basel SIB Swiss Institute of Bioinformatics Klingelbergstrasse 50-70 4056 Basel
[ccp4bb] Postdoc position at Imperial College
Please see the link below for details: http://www.jobs.ac.uk/job/AHH279/research-associate/
[ccp4bb] Position available in biomolecular simulation
Hi all, We have an opening for a computational scientist within my group at Daresbury (Cheshire, UK) to provide core support to the EPSRC-funded High-End Computing (HEC) Consortium in biomolecular simulation. The post will support the consortium through porting and optimisation of a variety of biomolecular simulation codes, with a focus on high performance computing. The post will also contribute to the development of a HEC toolkit designed to lower the barrier to the use of HEC resources. There may also be opportunities to contribute to science projects within the Daresbury group. Candidates must have strong programming skills and some experience of HEC systems. Further details are available at http://www.topcareer.jobs/Vacancy/irc108813_3575.aspx and you should also apply through that site (by 30th Sept). I am happy to take informal enquiries. Cheers Martyn * * Dr. Martyn Winn * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * Tel: +44 1925 603455 (DL) or +44 1235 567865 (RcaH) * E-mail: martyn.w...@stfc.ac.uk Skype: martyn.winn * -- Scanned by iCritical.
[ccp4bb] Two Postdoctoral Research Assistants in Oxford
We seek to appoint two Research Associates to undertake structural studies of the Tat protein transporter. The Tat system is a highly unusual protein transport pathway that moves folded proteins across the bacterial cytoplasmic membrane [Nature Rev.Microbiol. (2012) 10: 483]. The Tat system is required for the virulence of many bacterial pathogens. We have recently determined the structure of the core Tat transporter component TatC by X-ray crystallography [Nature (2012) 492: 210]. This project aims to build upon this success by determining high resolution structures of TatC in complex with other Tat components and with substrate targeting peptides. The project will also encompass related biochemical analysis of Tat complexes. Applicants must have an interest in structural biology and should possess, or expect to shortly obtain, a PhD in Biochemistry or Structural Biology or a related discipline. Applicants must have expertise in protein purification and characterisation as well as expertise in at least one of the following: X-ray crystallography or other high resolution structural method; working with membrane proteins; biochemical and biophysical analysis of protein-protein interactions; biochemistry of protein transport. These full-time posts are available immediately, working jointly with Professor Ben Berks in the Department of Biochemistry and Professor Susan Lea in the Sir William Dunn School of Pathology, South Parks Road, Oxford. The positions are funded by the Medical Research Council (MRC) for up to 48 months in the first instance. https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form Prof. Susan M. Lea tel: +44 1865 275181 Professor of Chemical Pathology Sir William Dunn School of Pathology, Oxford OX1 3RE UK Tutorial Fellow @ Brasenose College, Oxford OX1 4AJ
[ccp4bb] Job Posting: Software Release Engineer for SBGrid Consortium
POSITION TITLE: Software Release Engineer II SBGrid Consortium, Harvard Medical School JOB SUMMARY: SBGrid Consortium at Harvard Medical School (www.sbgrid.org) is a collaboration to provide the structural biology community with support for research computing. The primary service offered by SBGrid is the collection, deployment and maintenance of a comprehensive set of software and computational tools that are useful in structural biology research. The SBGrid software library is effectively a kind of scientific ‘app store’ that allows users to access a wide range of up-to-date applications without having to download, compile, configure, maintain or update software. Over 270 different scientific applications and software suites are supported on Linux and OS X operating systems. A paper describing the project was recently published in eLIFE (http://elife.elifesciences.org/content/2/e01456). PRIMARY JOB RESPONSIBILITIES: SBGrid Consortium has an immediate opening for a Software Release Engineer. The primary responsibilities of the position will be installing, configuring and testing structural biology software on Linux and OS X for use in the Consortium laboratories as well as providing first level technical support for software users. The majority of user support occurs over email, so the ability to communicate clear English instructions is critical. Additional responsibilities include working with scientific software developers to integrate new applications into the software collection. The scientific software is written in a polyglot of languages (Fortran, C, C++, Python, Java, Perl, Tcl/Tk and many sh/csh scripts) and built with any one of a number of different build systems (autotools, cmake, scons, homebrew shell scripts/makefiles, setuptools, etc). This is a hybrid type position where some software development experience is useful, but it is not a traditional developer job in any sense. You will work as a member of a multidisciplinary research and computing environment that integrates a software consortium, research computing support, research laboratories, and teaching initiatives. BASIC QUALIFICATIONS: Bachelor’s degree in computer science, computer engineering or technology-related discipline ; or PhD in Structural Biology; or equivalent combination of education plus relevant experience. 5-7 years of research computing experience. REQUIREMENTS: * basic working knowledge of at least one programming or scripting language * sh or csh shell scripting experience * basic knowledge of how to drive a compiler and linker as well as an understanding of shared libraries * autodidact with strong attention to detail and enthusiasm for hard problems ADDITIONAL QUALIFICATIONS: Familiarity with Python or other programming languages; familiarity with structural biology applications (e.g. PyMOL, Coot, Schrodinger) and structure determination/analysis workflows; strong knowledge of Linux and OS X operating systems. The successful candidate will have excellent organizational skills and particular ability to work independently and prioritize work. Proven project and/or program management skills. Excellent interpersonal and communications skills. Ability to work with discretion. TO APPLY, email the SBGrid Consortium at ap...@hkl.hms.harvard.edu. or go to the Harvard University job posting and apply online at https://sjobs.brassring.com/TGWEbHost/jobdetails.aspx?partnerID=25240siteID=5341AReq=30703BR
[ccp4bb] OT: Ribosomal processivity
Denizens of the bulletin board, I would like to tap into your vast knowledge of all things protein expression. Is anyone aware of a cell line or even a transformable/transfectable construct that produces high processivity ribosomes. I.E. one that can translate to the end of difficult mRNA without aborting prematurely? It doesn't have to be for E. coli. Yeast or Insect cells would be acceptable too. Any help would be appreciated. Cheers, Katherine -- Nil illegitimo carborundum* - *Didactylos
[ccp4bb] Structural transmission of signal across a membrane
Hello ccp4ers, I am helping a colleague develop a grant and have a vague recollection of structures of transmembrane protein receptors that signal across the membrane. Can anyone send me specific examples? Many thanks, G
Re: [ccp4bb] Structural transmission of signal across a membrane
Integrins? Loads of structures and models . On 24 Sep 2013 16:49, Edward A. Berry ber...@upstate.edu wrote: Gloria Borgstahl wrote: Hello ccp4ers, I am helping a colleague develop a grant and have a vague recollection of structures of transmembrane protein receptors that signal across the membrane. Can anyone send me specific examples? Many thanks, G I think cytoplasmic and periplasmic domains of the bacterial aspartate chemotaxis receptor (tar) were solved and a model of the whole protein was constructed.
Re: [ccp4bb] Structural transmission of signal across a membrane
Gloria Borgstahl wrote: Hello ccp4ers, I am helping a colleague develop a grant and have a vague recollection of structures of transmembrane protein receptors that signal across the membrane. Can anyone send me specific examples? Many thanks, G I think cytoplasmic and periplasmic domains of the bacterial aspartate chemotaxis receptor (tar) were solved and a model of the whole protein was constructed.
Re: [ccp4bb] OT: Ribosomal processivity
I forgot to mention that in this case gene optimization and eukaryotic expression don't help. It's a product of the protein sequence itself. On Tue, Sep 24, 2013 at 10:29 AM, Katherine Sippel katherine.sip...@gmail.com wrote: Denizens of the bulletin board, I would like to tap into your vast knowledge of all things protein expression. Is anyone aware of a cell line or even a transformable/transfectable construct that produces high processivity ribosomes. I.E. one that can translate to the end of difficult mRNA without aborting prematurely? It doesn't have to be for E. coli. Yeast or Insect cells would be acceptable too. Any help would be appreciated. Cheers, Katherine -- Nil illegitimo carborundum* - *Didactylos -- Nil illegitimo carborundum* - *Didactylos
